Integrating Ubuntu with a Windows-based network is harder than it should be

You talk about PhoneManager not working with Wine. Have you considered some alternatives? Many linux users (myself included) use vmware or kvm to run applications that don't work in wine, or don't work well in wine for which there are no alternatives available. I would recommend the first step here is to evaluate whether some over VoIP client for your phone system exists that will run in linux, if that won't work, check out using vmware to run it. you could also set up a 2x application server (www.2x.com) and share out that app.